2000 character limit reached
The exploration-exploitation paradigm for networked biological systems
Published 29 Jun 2023 in physics.bio-ph and q-bio.NC | (2306.17300v3)
Abstract: The stochastic exploration of the configuration space and the exploitation of functional states underlie many biological processes. The evolutionary dynamics stands out as a remarkable example. Here, we introduce a novel formalism that mimics evolution and encodes a general exploration-exploitation dynamics for biological networks. We apply it to the brain wiring problem, focusing on the maturation of that of the nematode C. elegans. We demonstrate that a parsimonious maxent description of the adult brain combined with our framework is able to track down the entire developmental trajectory.
- W. Bialek, Biophysics: searching for principles (Princeton University Press, 2012).
- J. F. Crow and M. Kimura, An introduction to population genetics theory (Scientific Publishers, 2017).
- V. Dichio, The exploration-exploitation paradigm: a biophysical approach, Phd thesis, Sorbonne Université (2023a).
- B. A. Hassan and P. R. Hiesinger, Cell 163, 285 (2015).
- R. A. Neher and B. I. Shraiman, Rev. Mod. Phys. 83, 1283 (2011).
- V. Dichio, H. Zeng, and E. Aurell, Reports on Progress in Physics 86, 052601 (2023).
- N. Goldenfeld and C. Woese, Annu. Rev. Condens. Matter Phys. 2, 375 (2011).
- M. d. Bono and A. Villu Maricq, Annu. Rev. Neurosci. 28, 451 (2005).
- A. Pathak, N. Chatterjee, and S. Sinha, PLoS computational biology 16, e1007602 (2020).
- A. Azulay, E. Itskovits, and A. Zaslaver, PLoS computational biology 12, e1005021 (2016).
- V. Dichio and F. De Vico Fallani, Reports on Progress in Physics 86, 102601 (2023).
- P. C. Mahalanobis, Proceedings of the National Institute of Sciences (Calcutta) 2, 49 (1936).
- F. Dyson, Nature 427, 297 (2004).
- M. B. Hamilton, Population genetics (John Wiley & Sons, 2021).
- F. Zanini and R. A. Neher, Bioinformatics 28, 3332 (2012).
- E. Mauri, S. Cocco, and R. Monasson, Europhysics Letters 132, 56001 (2021).
- R. Albert and A.-L. Barabási, Rev. Mod. Phys. 74, 47 (2002).
- E. T. Jaynes, Physical review 106, 620 (1957).
- C. J. Geyer, Statistical science , 473 (1992).
- D. R. Hunter, Social networks 29, 216 (2007).
- G. Rapti, Journal of Neurogenetics 34, 259 (2020).
- D. A. Colón-Ramos, Current topics in developmental biology 87, 53 (2009).
- A. Kessy, A. Lewin, and K. Strimmer, The American Statistician 72, 309 (2018).
- V. Dichio, EE-graph-dyn, GitHub folder (2023b).
Paper Prompts
Sign up for free to create and run prompts on this paper using GPT-5.
Top Community Prompts
Collections
Sign up for free to add this paper to one or more collections.